Soybean (Glycine max), one of the most important crops in the world, is an essential source of protein and oil with high nutritional value for human and animal consumption. To enhance our understanding of the biology of the soybean plant, it is essential to have accurate information regarding the expression of each of its 55,897 protein-coding genes. Here, we present “Tabula Glycine”, the soybean single-cell resolution transcriptome atlas. This atlas is composed of single-nucleus RNA-sequencing data of nearly 120,000 nuclei isolated from 10 different Glycine max organs comprising the entire soybean plant. These nuclei cluster into 157 different groups based on their transcriptomic profiles. Using spatial transcriptomic technology, laser-microdissection RNA-seq datasets, and comparative genomic approaches, we functionally annotated ~80% of these clusters. Focusing on the transcriptional patterns of the soybean transcription factors (TFs), we observed that their activity is sufficient to define most cell types and their organ of origin, supporting the idea that TFs are key descriptors of cell identity and function. This unprecedented level of resolution makes the Tabula Glycine a functional genomic resource and a useful tool for the plant and soybean communities.